In a semiconductor manufacturing process, integrated circuits (also referred to as “dies”) are fabricated in a die area on a semiconductor wafer. The semiconductor wafer goes through many processing steps before the dies are separated by cutting the semiconductor wafer. The processing steps can include lithography, etching, doping, grinding, blade cutting, die-sawing and/or depositing different materials. The processing steps can include wet and dry processing steps. Semiconductor wafers and/or separated dies can be stacked or bonded on top of each other to form a three-dimensional (“3D”) IC. For example, a semiconductor wafer with micro electrical devices formed within can be bonded to another semiconductor wafer with micro electrical-mechanical system (“MEMS”) devices formed within the wafer. After bonding, the wafers are cut or separated into bonded dies, which consists of devices from both wafers. In another example, a semiconductor wafer with MEMS devices formed within can also be bonded with another capping wafer that has cavities or recesses formed within. After bonding, the wafers are cut or separated into bonded dies, which consist of MEMS devices and a corresponding cap. During processing and bonding procedures, contaminants, chemicals, or residue may penetrate the die area and may adversely affect production yield of dies formed therein.